Materials from Blender to Three.JS: Colors seem to be different
Okay, I found the solution by myself.

The reason, why the colors are different in webgl is: the exporter makes use of the rgb values that blender provides. After a lot of research I found out, the rgb values in blender are not gamma corrected. The Hex values are gamma corrected.

Thats why the colors were correct, after I applied the corrected hex-code to the materials.

Since that is a very crappy workflow, I talked to a developer from my team and he did some research on the WebGLRenderer.

He found out that you can enable a property called "gammaOutput". If you do that, all colors get gamma corrected by the renderer.



SOLUTION

renderer.gammaOutput = true;




compared to the first image in my question you can see the webgl version isn't that dark and oversaturated anymore. The small difference you can still notice comes form the environment lightning in blender.